[gmx-users] Overriding Wildcard dihedraltypes

hubert santuz hubert.santuz at gmail.com
Thu Jan 9 18:00:44 CET 2014


First, thanks for your detailed response.
> Thanks for the question, and particularly the detail. It seems that you are
> trying use a [dihedraltypes] section in my_molecule.itp, which is generally
> a bad idea, because all such directives must appear before the first
> [molecule] directive, which defeats the point of molecule.itp files being
> somewhat movable. Because of that intention for molecule.itp files, there'd
> be no reason to have separate [dihedraltypes] sections that should be
> logically treated together, so the code assumes such sections are
> separable, and so you get unintended behaviour (perhaps particularly with
> wildcard atom types, and/or type 9 dihedrals) unless you change
> ffbonded.itp like you have now done.
By trying to simplify my problem, I have misleading you.
In fact, I have 2 itp files for my molecule (its is the cholesterol) :
   - One containing all the *types sections [atomtypes, bondtypes, 
dihedraltypes] (params_chol.itp)
  - The second one is a 'regular' itp file containing [molecules, atoms, 
bond ] sections. (cholesterol.itp)
So, in my topol. top, I have in reality this :

#include "charmm36.ff/forcefield.itp"
#include "params_chol.itp"
#include "cholesterol.itp"

My [dihedraltypes] directive is then before the [molecule] directive.
I have to do this because I have 2 new atoms for this molecule so I need 
to declare them somewhere. Therefore, I also need to declare the 
bondtypes, angletypes and dihedraltypes associated with these 2 new atoms.
All is working well except this dihedral override.
That's why I suspected a bug but maybe it is that part I'm not doing in 
the good way...
> Recommended procedures are
> * to copy the charmm36.ff directory into your working directory and modify
> ffbonded.itp to work like you want it to, or
> * to give explicit parameters in the [dihedrals] section of your
> molecule.itp (*not* [dihedraltypes]), so that the parameter lookup from
> [dihedraltypes] is not invoked at all. Note that the behaviour for multiple
> matching [dihedrals] is to add the functions; the behaviour for multiple
> matching [dihedraltypes] is to override earlier functions (except for type
> 9).
I'll try your second procedure and I'll let you know.
Thanks for the explanation between [dihedrals] and [dihedraltypes], I 
didn't know about it.

Best regards,

> On Thu, Jan 9, 2014 at 2:30 PM, hubert santuz <hubert.santuz at gmail.com>wrote:
>> Dear Gromacs Users,
>> I'm trying to set up a molecule into the charmm36 force field for lipids.
>> I correctly obtained a good itp file from a charmm file.
>> In this itp file, a wildcard dihedraltype (from the ffbonded.itp) is
>> overrided by an explicit dihedraltype :
>> In ffbonded.itp :
>> X    CTL1    CTL2    X    9    0.00    0.8368    3
>> In my itp file:
>> CRL1   CTL1   CTL2   CTL2     9    180.00       0.50961    3
>> CRL1   CTL1   CTL2   CTL2     9    180.00       0.91002    2
>> CRL1   CTL1   CTL2   CTL2     9    180.00       1.00332    1
>> In my topol.top:
>> #include "charmm36.ff/forcefield.itp"
>> #include "my_molecule.itp"
>> Unfortunately, this override is not taking in account by gromacs.
>> When I dump the tpr, I do not see this 3 types in the "functype" lines.
>> However, when I add this override into the ffbonded.itp file before the
>> wildcard dihedraltype like this :
>> In ffbonded.itp:
>> CRL1   CTL1   CTL2   CTL2     9    180.00       0.50961    3
>> CRL1   CTL1   CTL2   CTL2     9    180.00       0.91002    2
>> CRL1   CTL1   CTL2   CTL2     9    180.00       1.00332    1
>> X    CTL1    CTL2    X    9    0.00    0.8368    3
>> In this case, I can see clearly the 3 dihedraltypes in my tpr.
>> More interestingly, when I try to override an explicit dihedral type from
>> ffbonded.itp (like CEL1 CTL2 CEL1 HEL1) into my itp file, I get a warning
>> from grompp and I see the override in the tpr file.
>> It seems that wildcard dihedral types cannot be override (at least with
>> the function 9, I didn't test with other forcefields).
>> For the moment, the only solution that I have found is either to :
>>     - add the override in the ffbonded.itp which is not a good idea.
>>     - or add 2 new atoms with new names but with the same parameters than
>> (CTL1 and CTL2) in my itp file and change the dihedraltype according to
>> these two new atoms.
>> Without this override, I'm not able to reproduce the correct dihedral
>> energy from a SPE calculation between gromacs and namd... (but with the
>> override, I am!)
>> Have people already experienced this case ?
>> Also, I can provide test files (itp, top, pdb) with only 4 atoms and this
>> dihedral.
>> Thanks for the help!
>> Best regards,
>> Hubert
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